WholeGenomeReferenceSequenceMask (htsjdk 2.24.1 API)

java.lang.Object
- htsjdk.samtools.util.WholeGenomeReferenceSequenceMask

All Implemented Interfaces:

ReferenceSequenceMask
```
public class WholeGenomeReferenceSequenceMask
extends Object
implements ReferenceSequenceMask
```
Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.

Constructor Summary

Constructors
Constructor Description

WholeGenomeReferenceSequenceMask(SAMFileHeader header)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`get(int sequenceIndex, int position)`	It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
`int`	`getMaxPosition()`
`int`	`getMaxSequenceIndex()`
`int`	`nextPosition(int sequenceIndex, int position)`	It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - WholeGenomeReferenceSequenceMask
```
public WholeGenomeReferenceSequenceMask(SAMFileHeader header)
```
- Method Detail
  - get
```
public boolean get(int sequenceIndex,
                   int position)
```
    Description copied from interface: ReferenceSequenceMask
    
    It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
    
    Specified by:
    
    get in interface ReferenceSequenceMask
    
    Returns:
    
    true if the mask is set for the given sequence and position
  - nextPosition
```
public int nextPosition(int sequenceIndex,
                        int position)
```
    Description copied from interface: ReferenceSequenceMask
    
    It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
    
    Specified by:
    
    nextPosition in interface ReferenceSequenceMask
    
    Returns:
    
    the next pos on the given sequence >= position that is set, or -1 if there are no more set positions
  - getMaxSequenceIndex
```
public int getMaxSequenceIndex()
```
    Specified by:
    
    getMaxSequenceIndex in interface ReferenceSequenceMask
    
    Returns:
    
    Largest sequence index for which there are set bits.
  - getMaxPosition
```
public int getMaxPosition()
```
    Specified by:
    
    getMaxPosition in interface ReferenceSequenceMask
    
    Returns:
    
    the largest position on the last sequence index